Merge branch 'master' into data-contributor-guide

NCATSTranslator · Sep 26, 2024 · 20dddbc · 20dddbc
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diff --git a/docs/architecture/kp/index.md b/docs/architecture/kp/index.md
@@ -21,10 +21,11 @@ Knowledge Providers (KPs) contribute domain-specific, high-value information abs
 | Multiomics Provider     | BigGIM II-DrugResponse              | [BigGIM II-DrugResponse Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Big-GIM-II:-Drug-Response-KP)                   |                                                                                                                                                                                                |
 | Multiomics Provider     | Multiomics Wellness                 | [Multiomics Wellness Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Wellness-KP)                                       |                                                                                                                 |
 | Multiomics Provider     | EHR Clinical Risk                   | [EHR Clinical Risk Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/EHR-Risk-KP)                                         |                                                                                                                 |
-| Multiomics Provider     | Clinical Trials                     |                                                                                                                                      | [Hadlock-Lab/Multiomics_ClinicalTrials_KP](https://github.com/Hadlock-Lab/Multiomics_ClinicalTrials_KP)         |
+| Multiomics Provider     | Clinical Trials                     | [ClinicalTrials KP](https://github.com/NCATSTranslator/Translator-All/wiki/Clinical-Trials-KP)                 | [ClinicalTrials_KP](https://github.com/multiomicsKP/clinical_trials_kp)         |
+| Multiomics Provider     | Drug Approvals                     | [Drug Approvals KP](https://github.com/NCATSTranslator/Translator-All/wiki/Multiomics-Drug-Approvals-KP)                 | [Drug Approvals KP](https://github.com/multiomicsKP/drug_approvals_kp)         |
 | Expander Agent          | RTX-KG2                             | [RTX-KG2 Page](rtx-kg2.md)<br/>[RTX-KG2 Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/KG2)                            | [RTXteam/RTX-KG2](https://github.com/RTXteam/RTX-KG2)                                                           |
 | [Service Provider](../../teams/service-provider.md)        | Pathway Figure OCR                  | [Pathway Figure OCR Wiki](<https://github.com/NCATSTranslator/Translator-All/wiki/Pathway-Figure-OCR-(PFOCR)>)                       | [wikipathways/pathway-figure-ocr](https://github.com/wikipathways/pathway-figure-ocr)                           |
 | Exposures Provider      | ICEES                               | [ICEES Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Exposures-Provider-ICEES)                                        | [NCATS-Tangerine/icees-api](https://github.com/NCATS-Tangerine/icees-api)                                       |
 | Exposures Provider      | Causal Activity Model (CAM) KP      | [CAM-KP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/CAM-KP)                                                         | [NCATS-Tangerine/cam-kp-api](https://github.com/NCATS-Tangerine/cam-kp-api)                                     |
 | Genetics Provider       | Genetics Provider                   | [Genetics Provider Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Genetics-Knowledge-Provider)                         | [broadinstitute/genetics-kp-dev](https://github.com/broadinstitute/genetics-kp-dev)                             |
-| Connections Hypothesis Provider (CHP) | Connections Hypothesis Provider API ('CHP API') | [CHP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Connections-Hypothesis-Provider) | [di2ag/chp-api](https://github.com/di2ag/chp_api) |
+| Connections Hypothesis Provider (CHP) | Connections Hypothesis Provider API ('CHP API') | [CHP Wiki](https://github.com/NCATSTranslator/Translator-All/wiki/Connections-Hypothesis-Provider) | [di2ag/chp-api](https://github.com/di2ag/chp_api) |
diff --git a/docs/deployment-guide/monitoring.md b/docs/deployment-guide/monitoring.md
@@ -7,46 +7,107 @@ Ensuring the health and performance of the Translator system will require the ap
 
 # Endpoint uptime monitoring
 
-T.B.A. (Tim Putnam to elaborate)
+Uptime monitoring can easily be turned on for Translator applications, using [UptimeRobot](https://uptimerobot.com/). Uptime and outage events can be reported directly to Translator Slack channels.
+
+Contact Kevin Schaper for more information or to add new applications to monitor.
 
 # Telemetry
 
-Given the distributed nature of Biomedical Translator knowledge processing components, tracing the flow of queries through the system represents a challenge. Observability is the practice of measuring the state of a system by its various component outputs. [OpenTelemetry](https://opentelemetry.io/) is an open-source observability framework. Applying elements of OpenTelemetry to Translator will help in the challenge of query auditing, for quality assurance or performance.  An overview of OpenTelemetry concepts is provided [here](https://docs.google.com/presentation/d/1OjcE1gVhx8u9EvvHGn6h50otBKmpd-9HidlTNppXXy0/edit#slide=id.g27ee40efb83_0_3) and a small Translator demo of the concept using the Jaeger telemetry collector, is [here](https://github.com/TranslatorSRI/Jaeger-demo).
+Given the distributed nature of Biomedical Translator knowledge processing components, tracing the flow of queries through the system represents a challenge. Observability is the practice of measuring the state of a system by its various component outputs. [OpenTelemetry](https://opentelemetry.io/) is an open-source observability framework. Applying elements of OpenTelemetry to Translator helps with query auditing, quality assurance, and performance analysis.  
+
+The [documentation](https://opentelemetry.io/docs/what-is-opentelemetry/) provided by OpenTelemetry is the best place to learn the basics. An OpenTelemetry system is composed of at least two parts: a client that exports telemetry data and a backend that collects telemetry data. Translator teams should implement the client side (exporters) in their applications, but not necessarily a backend.
+
+Currently, Translator telemetry tools only support [traces](https://opentelemetry.io/docs/concepts/signals/traces/), not metrics or logs.
+
+### Telemetry Instrumentation and Protocols
+
+Translator components should [instrument](https://opentelemetry.io/docs/concepts/instrumentation/) their applications with a library that supports sending traces with the OpenTelemetry Protocol ([OTLP](https://opentelemetry.io/docs/specs/otel/protocol/)).
+
+For most applications, libraries are available that will automatically instrument your application, without manually implementing anything specific. This will usually be enough for Translator purposes. For example, you should not need to manually handle associating spans and traces with their parents. However, if you would like to customize the information collected, and make your trace information more useful, you may want to add [baggage](https://opentelemetry.io/docs/concepts/signals/baggage/) to traces.
+
+OTLP telemetry data can be sent over HTTP or gRPC. Both are supported by the Translator OpenTelemetry backend.
+
+Previously, Translator applications were instrumented using [Jaeger Client Libraries](https://www.jaegertracing.io/docs/1.61/client-libraries/), utilizing the Thrift protocol, but these libraries have been deprecated, in favor of OTLP.
+
+### Translator Deployment
+
+Translator tools should send telemetry data to shared backend applications deployed on ITRB servers. The backend applications are implemented using [Jaeger](https://www.jaegertracing.io/). In the ITRB Kubernetes cluster, each maturity level has its own instance of Jaeger deployed, so that telemetry data from all the applications in any given maturity level is aggregated in one place, but not mixed across maturities. This also allows us to configure OTEL clients to send data to a consistent host endpoint across maturity levels.
+
+Translator applications (clients) should configure their kubernetes deployments to send telemetry data to one of the following, and it should work for CI, test, and prod.
+
+HTTP
+jaeger-otel-collector:4318
+
+gRPC
+jaeger-otel-collector:4317
+
+To view telemetry data, the Jaeger UI can be accessed with the following links: 
+* [CI Jaeger](https://translator-otel.ci.transltr.io/search)
+* [Test Jaeger](https://translator-otel.test.transltr.io/search)
+* [Prod Jaeger](https://translator-otel.transltr.io/search)
+
+### Examples
+
+A simple demonstration of an OpenTelemetry implementation for python FastAPI servers is provided [here](https://github.com/TranslatorSRI/Jaeger-demo).
+
+OpenTelemetry also provides a demo application [here](https://opentelemetry.io/docs/demo/).
+
+Slides from the first Translator Relay session on OpenTelemetry can be found [here](https://docs.google.com/presentation/d/1OjcE1gVhx8u9EvvHGn6h50otBKmpd-9HidlTNppXXy0/edit#slide=id.g27ee40efb83_0_3).
+
 
 ### Telemetry Frequently Asked Questions
 #### When I instrument my application should I trace incoming requests or outgoing?
- In a microservices environment such as the Translator system, tracing both incoming and outgoing requests is key. Incoming tracing reveals user journeys, while outgoing tracing uncovers dependencies between services—both are crucial for comprehensive visibility and issue diagnosis.
+In a microservices environment such as the Translator system, tracing both incoming and outgoing requests is key. Incoming tracing reveals user journeys, while outgoing tracing uncovers dependencies between services—both are crucial for comprehensive visibility and issue diagnosis.
 
- As an example ARAGORN, an ARA that receives requests from the ARS and performs subsequent requests to downstream components makes use of FastAPI instrumentation to trace incoming requests and httpx instrumentation for tracing outgoing requests. This [code snippet](https://github.com/ranking-agent/aragorn/blob/main/src/otel_config.py) shows how ARAGORN traces both incoming and outgoing requests.
+As an example, ARAGORN, an ARA that receives requests from the ARS and performs subsequent requests to downstream components makes use of FastAPI instrumentation to trace incoming requests and httpx instrumentation for tracing outgoing requests. This [code snippet](https://github.com/ranking-agent/aragorn/blob/main/src/otel_config.py) shows how ARAGORN traces both incoming and outgoing requests.
 
-#### When tracing outgoing requests should it be logged if the request is bound to external services?
-Logging outgoing requests bound to external services can be essential for capturing communication details, aiding in troubleshooting, performance monitoring, and understanding dependencies outside your system.
+#### When tracing outgoing requests, should calls to external services outside of Translator components be included?
+Recording outgoing requests to external services can be essential for capturing communication details, aiding in troubleshooting, performance monitoring, and understanding dependencies outside your system.
 
 #### In a Development environment with no provisioned Jaeger instance, what is the best way to test my OTEL implementation?
 
 To use a local Jaeger instance for testing your OpenTelemetry implementation, you can follow these general steps:
 
-1. **Install Jaeger:** Download and install Jaeger locally. You can use Docker to quickly set up a Jaeger instance:
+1. **Install Jaeger:** Download and install Jaeger locally. You can use Docker to quickly set up a [Jaeger all-in-one](https://www.jaegertracing.io/docs/1.61/getting-started/#all-in-one) instance:
    ```bash
-      docker run -d --name jaeger -p 16686:16686 -p 6831:6831/udp jaegertracing/all-in-one:latest
+      docker run -d --name jaeger -p 16686:16686 -p 4317:4317 -p 4318:4318 jaegertracing/all-in-one:latest
    ```
    This command pulls the latest Jaeger image and runs it, exposing the Jaeger UI on port 16686.
-2. **Configure OpenTelemetry SDK:** Use the OpenTelemetry SDK in your application to send traces to your local Jaeger instance. Configure your OpenTelemetry instrumentation to send data to localhost    on the relevant Jaeger ports (usually 6831 for UDP and 16686 for HTTP).
+2. **Configure OpenTelemetry SDK:** Use the OpenTelemetry SDK in your application to send traces to your local Jaeger instance. Configure your OpenTelemetry instrumentation to send data to localhost on the relevant Jaeger ports (4318 for HTTP and 4317 for gRPC).
 
 3. **Instrument Your Code:** Instrument your application using OpenTelemetry APIs to create traces. Please make sure you've set up the instrumentation to export traces to your local Jaeger instance.
 
 4. **Verify Traces:** Execute your application's workflows or requests that should generate traces. Then, access the Jaeger UI at http://localhost:16686 in your browser to view the traces generated by your application.
 
-
 Remember to adapt the OpenTelemetry SDK configuration in your code to use the address and ports where your local Jaeger instance is running.
 
 This approach provides a local environment for testing OpenTelemetry traces with Jaeger without needing a remote Jaeger instance.
 
-Once ready for deployment, in the ITRB-managed environments Jaeger can be found at `jaeger-otel-agent.sri:6831`. This stays the same in all ITRB-managed environments, pointing to an instance in the environment where your application is deployed. 
+#### I already implemented OpenTelemetry using a Jaeger Client, but now I want to migrate to an OTLP client, what do I need to do?
 
-#### Where can I see my traces in ITRB environments once deployed?
-Jaeger UI can be accessed in the following links: 
-* [CI Jaeger](https://translator-otel.ci.transltr.io/search)
-* [Test Jaeger](https://translator-otel.test.transltr.io/search)
-* [Prod Jaeger](https://translator-otel.transltr.io/search)
+Due to the simplicity of most Translator telemetry implementations, migration from a Jaeger Client to an OTLP client should be fairly quick and straightforward. It may be as simple as replacing one of the packages used to instrument the application.
+
+You will also need to change the deployment configuration for where traces are sent. The Thrift protocol, and it's associated port (6831), will not work with OTLP. Use HTTP (port 4318) or gRPC (port 4317) instead.
+
+For example, in python, something like the following change may be all that is required. This example is not meant to be comprehensive or work as is, only to show relevant changes. The host and the port should come from environment variables or some deployment configuration instead of being hardcoded.
+
+```python
+from opentelemetry.exporter.jaeger.thrift import JaegerExporter
+
+jaeger_exporter = JaegerExporter(
+    agent_host_name="localhost",
+    agent_port=6831
+)
+processor = BatchSpanProcessor(jaeger_exporter)
+```
+vs
+```python
+from opentelemetry.exporter.otlp.proto.grpc.trace_exporter import OTLPSpanExporter
+
+otlp_exporter = OTLPSpanExporter(endpoint="localhost:4317")
+processor = BatchSpanProcessor(otlp_exporter)
+```
+
+#### Can I use a [zero-code](https://opentelemetry.io/docs/concepts/instrumentation/zero-code/) instrumentation?
 
+Yes, you can, and it may be the fastest way to instrument your application. However, if you decide to add custom baggage, or to change default instrumentation details, you will probably need to re-instrument your application using code.